qctools is a toolkit for ensuring critical files are reviewed on a project. It manages the quality control (QC) process by tracking the assignment and acceptance of files using a centralized log file, QClog.csv. Along with tracking QC, qctools provides additional tooling for code review and comparing outputs such as figures and tables.
By integrating with Git, qctools automatically detects when a file has been modified and flags it for re-evaluation. It provides functions to check outstanding QC and summarize the QC status of all files.
The core functions of qctools are:
logCreate(): Creates the QC log.logAssign(): Assigns files to reviewers for QC.logAccept(): Marks files as reviewed and accepted.logPending(): Lists files that still need QC.logSummary(): Provides a high-level summary of the QC status of all files.logCreate()
To create a QC log, use logCreate(). This will generate the QClog.csv file at the top level of the project.
For demonstration, assume the QClog.csv already contains some entries.
| file | commit | reviewer | datetime |
|---|---|---|---|
| script/analysis.R | Initial-Assignment | Jane Doe | 2024-11-19 10:00:00 |
| script/data-prep.R | abc1234 | John Smith | 2024-11-19 11:30:00 |
| script/visualize.R | def5678 | Bob Miller | 2024-11-19 13:00:00 |
logAssign()
Suppose we are the author of script/model-fitting.R and it is ready for review. We can assign script/model-fitting.R to Alice Johnson for QC. Below is the code for this operation and the updated log.
logAssign(file = "script/model-fitting.R", reviewer = "Alice Johnson")| file | commit | reviewer | datetime |
|---|---|---|---|
| script/analysis.R | Initial-Assignment | Jane Doe | 2024-11-19 10:00:00 |
| script/data-prep.R | abc1234 | John Smith | 2024-11-19 11:30:00 |
| script/visualize.R | def5678 | Bob Miller | 2024-11-19 13:00:00 |
| script/model-fitting.R | Initial-Assignment | Alice Johnson | 2024-11-19 14:00:00 |
logAccept()
After Alice Johnson reviews script/model-fitting.R, she can accept the file by using logAccept().
logAccept(file = "script/model-fitting.R")| file | commit | reviewer | datetime |
|---|---|---|---|
| script/analysis.R | Initial-Assignment | Jane Doe | 2024-11-19 10:00:00 |
| script/data-prep.R | abc1234 | John Smith | 2024-11-19 11:30:00 |
| script/visualize.R | def5678 | Bob Miller | 2024-11-19 13:00:00 |
| script/model-fitting.R | Initial-Assignment | Alice Johnson | 2024-11-19 14:00:00 |
| script/model-fitting.R | ghi9012 | Alice Johnson | 2024-11-19 15:00:00 |
logPending()
Suppose we want to view all files with oustanding QC needs. logPending() lists files that require QC because they are either:
An example output of logPending() is shown below.
| file | last_author | reviewer | datetime |
|---|---|---|---|
| script/analysis.R | Bob Miller | Jane Doe | 2024-11-19 10:00:00 |
logSummary()
If we want to see the QC status of all files in the log, we can use logSummary() to do so.
| file | status |
|---|---|
| script/analysis.R | Modified - needs QC |
| script/data-prep.R | Fully QCed |
| script/model-fitting.R | Fully QCed |
| script/visualize.R | Fully QCed |
Create the log (once per project):
Assign files for review:
logAssign(file = "script/model-fitting.R", reviewer = "Alice Johnson")Mark files as accepted after review:
logAccept(file = "script/model-fitting.R")Display files with oustanding QC:
View the QC status of all files in the QC log:
If you encounter a clear bug, please file an issue with a minimal reproducible example on the qctools/issues page.